The current thing isn't a flashback, so to speak. We're just going into the story of how Mimi became Her. I guess GT WHAM could be considered the current storyline, then this is an off shoot.

Flashbacks are an insanely popular way to tell stories, especially for most web comics. Like The Zombie Hunter's Comic. THE biggest god damn flash back that I've ever seen. Its a great way to tell a story or provide background information, but its also the easiest.

I was actually thinking more along the lines of the last boss from Mega Man X8, especially since the visual motif of the monitors and globes are highly reminiscent of the stage select screen in that game. I do see where the perspective and arrangement, though, are more like the Zero 1 final boss (that I was never able to beat).